| Title: | ExperimentHub datasets for the nullranges package |
|---|---|
| Description: | Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package. |
| Authors: | Michael Love [aut, cre] (ORCID: <https://orcid.org/0000-0001-8401-0545>), Wancen Mu [aut] (ORCID: <https://orcid.org/0000-0002-5061-7581>), Eric Davis [aut] (ORCID: <https://orcid.org/0000-0003-4051-3217>), Mikhail Dozmorov [aut] |
| Maintainer: | Michael Love <[email protected]> |
| License: | GPL-3 |
| Version: | 1.18.0 |
| Built: | 2026-10-10 11:16:12 UTC |
| Source: | https://github.com/bioc/nullrangesData |
An example dataset containing narrowPeak file from ENCODE. Retrieve
record with object[["AH22505"]] on Annotation Hub. Construction
script is in 'inst/script/DHSA549Hg38.R'. Function returns a GRanges
object with metadata score, signal value, p/q value and peak.
dhs <- DHSA549Hg38() dhsdhs <- DHSA549Hg38() dhs
10Kb bins were tiled across hg19 and annotated with CTCF and DNase site features from GM12878. Feature annotations for each bin include 1) the number of CTCF sites, 2) the CTCF signal strength (from peak calls), 3) the number of DNase sites, 4) the DNase signal strength (from signal tracks), and finally 5) the presence/absence of a loop to any other bin. Function returns a GRanges object with covariate metadata
bins <- hg19_10kb_bins() binsbins <- hg19_10kb_bins() bins
10Kb bins were tiled across hg19 then subset by those which contained CTCF sites. All pairs of CTCF-bound 10Kb bins were generated and annotated with feature overlaps from GM12878. Feature annotations include 1) presence/absence of a loop between bin-pairs, 2) the total CTCF signal from both bin-pairs, 3) the number of CTCF sites from both bin-pairs, 4) the distance between bin-pairs, and finally 4) whether a convergent set of CTCF sites exists between bin-pairs. Function returns a GInteractions object with covariate metadata
binPairs <- hg19_10kb_ctcfBoundBinPairs() binPairsbinPairs <- hg19_10kb_ctcfBoundBinPairs() binPairs
DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions for demonstration of functions in the nullranges package.
suppressPackageStartupMessages(library(GenomicRanges)) dhs <- DHSA549Hg38() dhssuppressPackageStartupMessages(library(GenomicRanges)) dhs <- DHSA549Hg38() dhs
An example dataset of Single cell Gene and ATAC-seq data for Construction script is in 'inst/script/make-multiome-data.R'. Function returns a promoter GRanges object with pseudo bulk counts stored in metadata column "counts2" as NumericList.
data("sc_promoter")data("sc_promoter")
An example dataset of Single cell Gene and ATAC-seq data for Construction script is in 'inst/script/make-multiome-data.R'. Function returns a gene expression GRanges object with pseudo bulk counts stored in metadata column "counts1" as NumericList.
data("sc_rna")data("sc_rna")